Makoto Naegi is such a great character because he’s literally just some guy. His just a guy syndrome is so incrediblly large but he makes it work!! That’s the whole point. I feel like a lot of people get the very basic idea of Makoto Naegi as a character (that he is nice :)) and that he has hope !!), but don’t bother to dig deeper. Which is fair I don’t think the writers bothered to either. Makoto is stubborn, and I personally feel like that’s a flaw of his. Despite the fact that the remnants of despair are obviously dangerous people and terrorists, despite the fact that his boss and coworkers tell him not to, he goes behind their backs and does it anyway, because he hopes and believes that they still have good in them!! And this is his greatest strength and greatest weakness!! AND he sweet talks Kyoko and Byakuya into helping him, hes emotionally skilled enough to convince them against rational thinking. I’m not saying he’s manipulative or anything, just that I could see him managing to convince them because that’s just a part of his character.
The games and anime don’t give me much, but I definitely see Makoto as somebody who will see things through if he believes in them enough, no matter what anybody else says. He has set ideals and gdi if he thinks the ROD can be saved then god damnit it guys we’re gonna try. And even if it wasn’t directly his fault people still got hurt because of his actions!! But it’s fine because the entire time Makoto was optimistic and had full belief that things would work out. And they did. Technically, he was right. And that can be such an interesting aspect of his character!!